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Diversity of VP7, VP4, VP6, NSP2, NSP4, and NSP5 genes of porcine rotavirus C: phylogenetic analysis and description of potential new VP7, VP4, VP6, and NSP4 genotypes

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Abstract

Rotavirus C (RVC) is a cause of gastroenteritis in swine and has a worldwide distribution. A total of 448 intestinal or faecal samples from pigs of all ages were tested for viruses causing gastroenteritis. RVC was detected in 118 samples (26.3 %). To gain information on virus diversity, the complete coding nucleotide sequences of the VP7, VP4, VP6, NSP2, NSP4, and NSP5 genes of seven RVC strains were determined. Phylogenetic analysis of VP7 nucleotide sequence divided studied Czech strains into six G genotypes (G1, G3, G5-G7, and a newly described G10 genotype) based on an 85 % identity cutoff value at the nucleotide level. Analysis of the VP4 gene revealed low nucleotide sequence identities between two Czech strains and other porcine (72.2-75.3 %), bovine (74.1-74.6 %), and human (69.1-69.3 %) RVC strains. Thus, we propose that those two Czech porcine strains comprise a new RVC VP4 genotype, P8. Analysis of the VP6 gene showed 79.9-86.8 % similarity at the nucleotide level between the Czech strains and other porcine RVC strains. According to the 87 % identity cutoff value, we propose the existence of three new RVC VP6 genotypes, I8-I10. Analysis of the NSP4 gene divided porcine RVC strains into two clusters (the E1 genotype and the new E4 genotype, based on an 85 % nucleotide sequence identity cutoff value). Our results indicate a degree of high genetic heterogeneity, not only in the variable VP7 and VP4 genes encoding the outer capsid proteins, but also in more-conserved genes encoding the inner capsid protein VP6 and the non-structural proteins NSP2, NSP4, and NSP5. This emphasizes the need for a whole-genome-sequence-based classification system.

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Acknowledgments

We thank Andrea Kyjovská and Andrea Ďurišová for their skilful technical assistance, and Miroslav Toman for helpful discussion during the manuscript preparation. Results of the study were obtained with financial support from the Ministry of Education, Youth and Sports of the Czech Republic (project LO1218 under the NPU I program).

Conflict of interest

The authors declare that they have no actual or potential conflict of interest.

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Authors and Affiliations

  1. Veterinary Research Institute, Hudcova 70, 621 00, Brno, Czech Republic

    Romana Moutelíková, Jana Prodělalová & Lucie Dufková

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  1. Romana Moutelíková
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  2. Jana Prodělalová
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Corresponding author

Correspondence to Romana Moutelíková.

Additional information

The GenBank accession numbers for the porcine RVC sequences reported in this paper are KF036287, KM099247-KM099271, and KP776735-KP776743 as specified in supplementary table (Online Resource 2).

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Moutelíková, R., Prodělalová, J. & Dufková, L. Diversity of VP7, VP4, VP6, NSP2, NSP4, and NSP5 genes of porcine rotavirus C: phylogenetic analysis and description of potential new VP7, VP4, VP6, and NSP4 genotypes. Arch Virol 160, 1715–1727 (2015). https://doi.org/10.1007/s00705-015-2438-7

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